My dog is 12/13 and never had a problem in our apartment, but now when we are in a townhouse, she does have problems. I assume it's confusion and separation anxiety, but how can I get her to stop this behavior? She even pees sometimes when I am upstairs and she is downstairs!

Make sure you let her out maybe once an hour or so, or if she has a trigger word you can ask like "potty" and she reacts to it, then it probably means she has to go. If she doesn't have a trigger word then make one for her, every time you take her outside make sure you tell her toe word, and when she's done, associate the desired word with her going to the bathroom outside. Make sure she knows that outside is where the potty happens.

Also, Just so you know, rubbing her nose in it will not help anything, contrary to what many people say, it can cause her to become aggressive and distrusting. So PLEASE, do not rub her nose in it, and don't spank her. It will not regester that way.

Make sure you train her by encouraging her. If you catch her going, firmly say no and direct her outside. When she is finished praise her. Keep treats on hand for this.
What she will learn is that going potty outside gives her treats, and she likes treats, so she will go potty outside! Good luck!

I'm sure Shazamataz might find this and give her input as well, she's the dogs expert here!

How old is she?

If she is 12+ years old, it could be age related. A trip to the vet for a check up may help determine if it symptoms of aging that have just become more noticeable with the move.

Ohso, great post on puppy training. :)